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- PDB-2gle: Solution structure of neurabin SAM domain -

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Basic information

Entry
Database: PDB / ID: 2gle
TitleSolution structure of neurabin SAM domain
ComponentsNeurabin-1
KeywordsPROTEIN BINDING / SAM domain / Scaffold / Protein protein interaction
Function / homology
Function and homology information


growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of actin filament polymerization ...growth cone lamellipodium / negative regulation of spontaneous neurotransmitter secretion / regulation of synapse structural plasticity / positive regulation of long-term synaptic depression / cellular response to toxic substance / postsynaptic actin cytoskeleton organization / postsynaptic actin cytoskeleton / protein phosphatase 1 binding / regulation of filopodium assembly / regulation of actin filament polymerization / regulation of dendritic spine morphogenesis / positive regulation of dendritic spine development / negative regulation of stress fiber assembly / regulation of synapse assembly / cortical actin cytoskeleton / dendritic spine neck / negative regulation of long-term synaptic potentiation / neuron development / excitatory postsynaptic potential / filopodium / actin filament organization / calcium-mediated signaling / modulation of chemical synaptic transmission / neuromuscular junction / positive regulation of neuron projection development / neuron projection development / actin filament binding / actin cytoskeleton / GTPase binding / lamellipodium / growth cone / transmembrane transporter binding / dendritic spine / postsynaptic density / cytoskeleton / protein domain specific binding / dendrite / neuronal cell body / glutamatergic synapse / protein-containing complex binding / protein kinase binding / identical protein binding / cytoplasm
Similarity search - Function
Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain ...Neurabin-1/2, PDZ domain / Neurabin-like family / PDZ domain / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsJu, T. / Hudak, J. / Peti, W.
CitationJournal: TO BE PUBLISHED
Title: Structural characterization of the neurabin SAM domain
Authors: Ju, T. / Ragusa, M.J. / Hudak, J. / Nairn, A.C. / Peti, W.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurabin-1


Theoretical massNumber of molelcules
Total (without water)8,3541
Polymers8,3541
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Neurabin-1 / Neurabin-I / Neural tissue-specific F-actin-binding protein I / Protein phosphatase 1 regulatory ...Neurabin-I / Neural tissue-specific F-actin-binding protein I / Protein phosphatase 1 regulatory subunit 9A / p180 / PP1bp175


Mass: 8353.628 Da / Num. of mol.: 1 / Fragment: SAM domain (residues 986-1056)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O35867

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
1332D NOESY
NMR detailsText: Cryo Probe

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM Neurabin SAM U-15N,13C, 20mM phosphate buffer Na, pH 6.8, 90% H2O, 10% D2O90% H2O/10% D2O
22mM Neurabin SAM U-15N, 20mM phosphate buffer Na, pH 6.8, 90% H2O, 10%90% H2O/10% D2O
32mM Neurabin SAM, 0mM phosphate buffer Na, pH 6.8, 100 % D2O100% D2O
Sample conditionsIonic strength: 50 mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Brukercollection
TopSpin1.3Brukerprocessing
CARA1.5Kellerdata analysis
ATNOS1.1Herrmannstructure solution
CYANA2Guntertstructure solution
CNS1.1Brungerrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1 / Details: RECOORD scripts, CNS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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